[eluser]Mitchell[/eluser]
The email class configuration can be set by adding a /config/email.php file with an array $config[]. However, if the Email class is extended (MY_email.php), then the configuration array is not used.
I have not been able to determine the root cause, but with no email extended class, Email.php function CI_Email() will be passed the correct $config array. With the email class extended, the $config array passed to CI_Email is null.